X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=cf383acc37dc9cee9b9d9633d4c5fcf478d88a50;hb=b03ab64755cdfd11f8d1f2c93d01f276d121e6d7;hp=5e09da79a02e66e6db05fec25a2b206e0c5c14dc;hpb=3402d066dbd7667cd805e6d78ac5eca66e237c72;p=jalview.git

diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 5e09da7..cf383ac 100755
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -44,8 +44,13 @@ public class AlignmentPanel
   // this value is set false when selection area being dragged
   boolean fastPaint = true;
 
+  boolean MAC = false;
+
   public AlignmentPanel(AlignFrame af, final AlignViewport av)
   {
+    if(System.getProperty("os.name").startsWith("Mac"))
+      MAC = true;
+
     alignFrame = af;
     this.av = av;
     seqPanel = new SeqPanel(av, this);
@@ -167,6 +172,9 @@ public class AlignmentPanel
     hscrollFillerPanel.setSize(d);
 
     alignFrame.pack();
+
+    if(overviewPanel!=null)
+          overviewPanel.updateOverviewImage();
   }
 
   public void setIdWidth(int w, int h)
@@ -274,6 +282,7 @@ public class AlignmentPanel
 
   public void setWrapAlignment(boolean wrap)
   {
+    av.startSeq = 0;
     scalePanelHolder.setVisible(!wrap);
     hscroll.setVisible(!wrap);
     idwidthAdjuster.setVisible(!wrap);
@@ -288,29 +297,6 @@ public class AlignmentPanel
 
   }
 
-  public void setColourScheme()
-  {
-    ColourSchemeI cs = av.getGlobalColourScheme();
-
-    if (av.getConservationSelected())
-    {
-
-      Alignment al = (Alignment) av.getAlignment();
-      Conservation c = new Conservation("All",
-                                        ResidueProperties.propHash, 3,
-                                        al.getSequences(), 0,
-                                        al.getWidth());
-
-      c.calculate();
-      c.verdict(false, av.ConsPercGaps);
-      ConservationColourScheme ccs = new ConservationColourScheme(c, cs);
-
-      av.setGlobalColourScheme(ccs);
-
-    }
-
-    repaint();
-  }
 
   int hextent = 0;
   int vextent = 0;
@@ -452,7 +438,7 @@ public class AlignmentPanel
       overviewPanel.setBoxPosition();
     }
 
-    if (av.getWrapAlignment() || !fastPaint)
+    if (av.getWrapAlignment() || !fastPaint || MAC)
     {
       repaint();
     }
@@ -482,13 +468,8 @@ public class AlignmentPanel
     idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
     annotationSpaceFillerHolder.setSize(d.width,
                                         annotationPanel.getSize().height);
-    alabels.setSize(d.width, annotationPanel.getSize().height);
 
-    alabels.repaint();
-    idPanel.idCanvas.repaint();
-    seqPanel.seqCanvas.repaint();
-    scalePanel.repaint();
-    annotationPanel.repaint();
+    alabels.setSize(d.width, annotationPanel.getSize().height);
 
     if (av.getWrapAlignment())
     {
@@ -504,5 +485,11 @@ public class AlignmentPanel
       setScrollValues(av.getStartRes(), av.getStartSeq());
     }
 
+    alabels.repaint();
+    idPanel.idCanvas.repaint();
+    seqPanel.seqCanvas.repaint();
+    scalePanel.repaint();
+    annotationPanel.repaint();
+
   }
 }